Genetic material may be analyzed by placing DNA (Deoxyribonucleic acid) material in an array of wells (dots). Polymerase chain reaction (PCR) amplification is often used in genetic analysis, where the PCR amplification augments the amount of DNA material placed in a well. Fluorescent dyes, such as CY3 or CY5, may be added to the DNA material, so that it fluoresces when excited by monochromatic light. Because with PCR amplification there may be different growth rates of DNA material from well to well, sample and reference channels may be set up whereby in each well, there is reference DNA and sample DNA. Fluorescent dye of one type may be used for the sample DNA, and fluorescent dye of another type may be used for the reference DNA.
This method also reduces the sources of variability and noise due to various aspects of an individual spot that affect both specimens (DNA sample and reference) similarly. In order to accurately calculate the density of the sample DNA material in a particular well after PCR amplification, the integral of the total fluorescence intensity (presumably representing the density of the DNA material inside the well) from the topological profile of the well is usually computed. The logarithmic value of the ratio of the two intensities of the fluorescent dye labeled specimens (one value for the sample specimen, the other value for the reference specimen) measured from the same well is calculated based on the assay's fluorescence image. The ratio of the two intensities would provide the normalized population of the gene material in the well, disregarding the initial population density.
In most of the available commercial solutions, the assay's fluorescence image is usually scanned by a color scanner with high resolution and then transferred to a computer for image analysis. The profile analysis software usually computes the normalized intensity of each well sequentially. The intensity of the fluorescence is usually relatively low. Using higher excitation light intensity or increasing detection time may lead to brighter fluorescence patterns. However, lower power consumption and faster detection may be preferable. Furthermore, some fixed-pattern noises in the input pattern may exist (e.g., fixed pattern noises created by scattered lights, or non-uniformity of the detector array response). These noises may introduce errors in the measurement of the density of the DNA materials
The development of low-cost portable instruments for rapidly analyzing genetic assays in noisy environments and with relatively low intensity of fluorescence would be of utility in medical services.